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I am just learning how to work with Armatures and need some help.

I made a simple armature and created vertex groups for each bone from bone heat, now I am weight painting the groups to get the deform right. However, I have noticed a couple of strange things : 1) The armature does not move in sync with my mesh ( see the screen shot), it has a delayed movement. 2) I put an IK constaint on the legs and added a knee bone to control the bending of the leg , but the deform at the knee is very strange ( see the screen shot).

Bending problem could be due to not enough faces surrounding the joint. A good (minimum) rule of thumb is to create three rows of faces at any joint point - one row where you want the joint, one row above and another row below. This should result in a more defined bend (more rows of faces will provide even more control and definition, to a point). Also be certain the connection between bones is exactly where you want the joint to bend.

Tcooper : The problem is the bones aren't following the Mesh. The Bones are deforming the Mesh, but move more slowly and don't stay inside of the Mesh.
Revoltrandy: How can I make sure I have all the modifiers turned of ? I don't think I have more than one, in the above file I just have the mesh parented to the armature and an IK constraint with a pole target for the knee.

In the above screenshot, in the buttons window (where the render buttons are), switch to 'editing' (the square icon with 4 dots at the corners), select the mesh, and there will be a panel with 2 tabs - 1 is modifiers - the other is shapes. Click on the modifiers tab and scroll thru the modifiers looking for ones name armature. If you have more than one, delete all extras by clicking on the X in the right side.

revolt_randy : Thanks, that solved the deform problem. I had used the hot key to Parent the mesh to the Armature, yet there was an Armature modifier on also - I don't understand the difference, or even how I added it accidentally ! It also apparently solved the other problem.... thanks again.

OK, I have a new problem I am posting a pic and the file.
The problem is that my foot keeps rotating when I try to take a step forward. Everything seemed fine until I got to the point of needing to grab the root bone and move the mesh forward to complete the step. The left leg worked fine, but as I move with the root bone, the right leg rotates.

I see what u mean... The lazy way i would do it would be 2 NOT move him forward, but anamate his walk, then go into object mode and anamate the armature sliding forward.
here's a vid of what i mean:
TURN UP UR VOLUME i am a mouse

Programming is 1% solving intricate problems with clever solutions and 99% hitting the compile button and having no idea why your program just did what it did.

I have tried to lock the rotation in the transform properties panel, but that doesn't stop his leg from rotating. Maybe I misunderstand the purpose of that panel or the lock button? I can't move him forward with the root bone without his leg twisting around.

I have tried to lock the rotation in the transform properties panel, but that doesn't stop his leg from rotating. Maybe I misunderstand the purpose of that panel or the lock button? I can't move him forward with the root bone without his leg twisting around.

A bone under IK constraint uses a different set of "locking" controls than a non-IK bone. Did you lock the bone in the correct place?

Thanks kastoria, I will have to look for that, but I am using an older version of Blender- 2.48a, to be precise ( because my computer is old and I can't seem to get the new versions to load install.) If you know where that panel is in my version, let me know. Thanks.

OK... I found the panel for the Ik constraint and beside it is a panel for the armature bones and with the shin bone selected (which is the bone that has the IK on it) it shows some options for locking or limiting. Is that the right panel? If it is, it doesn't seem to do anything either.
I have solved the rotating leg problem by turning off the Knee bone Pole Target. Apparently as the leg goes forward, the knee bone moves behind the leg and since that is the pole target, the leg twists to face it. Is there a way to lock the knee bone pole target in place? Do I need the pole target? Do other animators tend to use it?
Ok, third question : What in the world is that thing stretching from my feet to the floor plane?? Is it a plane or vertex? I have a plane for the floor, but I don't think it is that. I deleted the floor plane and the weird stretching things are still there... Heeeelllppp!

OK... I found the panel for the Ik constraint and beside it is a panel for the armature bones and with the shin bone selected (which is the bone that has the IK on it) it shows some options for locking or limiting. Is that the right panel? If it is, it doesn't seem to do anything either.

That looks like the same settings that are present in 2.5+. I have not used them much myself, and I have never used 2.4x so I'm not sure if there is something else that might affect how they behave.

I have solved the rotating leg problem by turning off the Knee bone Pole Target. Apparently as the leg goes forward, the knee bone moves behind the leg and since that is the pole target, the leg twists to face it. Is there a way to lock the knee bone pole target in place? Do I need the pole target? Do other animators tend to use it?

Yes, you need a pole target. If you don't have a pole target then you won't have a way to control where the knee is pointing. If you try to make this character walk without a pole target the legs will just look like they are made from spaghetti.

You have a couple ways to manage the pole target. You can just be sure that if you are going to move an foot IK target than you also highlight the pole target when you are moving the IK target forward. That should keep the pole target in front of the foot. Another option is to include some root bones in the model. These are bones that don't deform the model and exist simply to make it easier to move other groups of bones around. For example if you had a bone that was a parent of the IK target and the pole target then you could gab just that 'root' bone and move it forward to move both bones at the same time.

Another option is to just manually move the pole target forward when the knee is getting close to it.

Ok, third question : What in the world is that thing stretching from my feet to the floor plane?? Is it a plane or vertex? I have a plane for the floor, but I don't think it is that. I deleted the floor plane and the weird stretching things are still there... Heeeelllppp!

It looks like a weight painting issue. Leave the model in the posed position and find the bone in the armature that is closest to the heel of the foot. Then go into weight painting and see if you can assign some weight to that vert for the heel bone. If this is the problem, then the vert should just snap right back into the model.

The pole targets are right in front of the knees - in edit mode, move them forward a bit. As is, when the foot controller is raised, the knee bends and the pole target is behind the knee. If you move the pole target forward so it will always be in front of the knee, you should be fine. I see they are parented to the foot controller bones, which is nice as they will always move as the foot moves, and if you rotate the foot left to right, the pole target & knee will always follow, which is also nice. Another option is to parent them to the hip bone, or for your model, the bone sticking out of the back, as that is the bone you'd move to move the whole character forward. But then they would never follow the foot rotation, they would follow the body rotation. It's really just a matter of choice.

While I was looking at your file, I tried to cause the problem you posted, with the spike sticking out of the foot and couldn't, but in the process, I noticed this:
Looks like the verts in that area are not joined together, causing the tearing in the crotch. Locate the verts, alt-m -> merge at center to fix.

Yikes... didn't even notice that one... I have not even gotten to the point of going over all the weights on the vertex groups either. So I know there are lots of problems. I have been preoccupied with the problems I have posted.

Ok, I have a new problem : I am seeing little pink dots, the kind like tell you where an objects center is, and they are not in the center of my mesh. When I animated the mesh and the character goes foward, the centers stay behind. They are for the mesh and the armature, as you can see from the pic. I tried to center new but it still stays behind, also I don't know how or if you can center new for an armature...is it supposed to do this?

Yes, perfectly normal. Don't understand the reason for it and AFAIK there is no way to disable it either. However, seeing your screenshot I am reminded of the golden rule to rigging in blender - Your armature & mesh should have the same point of origin (or the same location), they should also have the same rotation and scale - to avoid problems. Check these by opening the transforms panel in the 3d view - n-key - and selecting each in object mode. To correct this, set the armature into rest pose. Snap the cursor to the armature (in object mode with armature selected, shift-s -> cursor to selected. Then select the mesh in object mode, in the object menu there should be a transform menu - choose origin to 3d cursor.